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Proto-Germanic(s) genetically and linguistically arose from an Indo-European component from the Pontic-Caspian steppe and a substrate Neolithic farmer component, itself being made up of an intrusive component originally from Anatolia and earlier Hunter Gatherers already living in Europe.

At least linguistically the Hunter Gatherer component seems to be restricted to Germanic and Balto-Slavic, however:

Seems like the Anatolian hypothesis about Indo-European culture and language having arrived with Neolithic farmers can finally be laid to rest.

It's also always refreshing, when modern science is “dumbfounded” by having to admit that much earlier physical and cultural anthropologists were largely right, despite having infinitely more “primitive” research means at hand.

Re-theorising mobility and the formation of culture and language among the Corded Ware Culture in Europe

Abstract
Recent genetic, isotopic and linguistic research has dramatically changed our understanding of how the Corded Ware Culture in Europe was formed. Here the authors explain it in terms of local adaptations and interactions between migrant Yamnaya people from the Pontic-Caspian steppe and indigenous North European Neolithic cultures.

The original herding economy of the Yamnaya migrants gradually gave way to new practices of crop cultivation, which led to the adoption of new words for those crops. The result of this hybridisation process was the formation of a new material culture, the Corded Ware Culture, and of a new dialect, Proto-Germanic. Despite a degree of hostility between expanding Corded Ware groups and indigenous Neolithic groups, stable isotope data suggest that exogamy provided a mechanism facilitating their integration. This article should be read in conjunction with that by Heyd (2017, in this issue).[...]

Re-theorising migrations

The evidence from the recent studies of ancient DNA documenting human migrations into temperate Europe during the early third millennium BC can be summarised as follows:

There was a widespread process of genetic admixture, leading to a reduction of Neolithic DNA in temperate Europe and the dramatic increase of a new genomic component that was only marginally present in Central Europe prior to 3000 BC (Allentoft et al. 2015; Haak et al. 2015; Cassidy et al. 2016).

Although the details of this admixture event can and will be debated for years to come (Vander Linden 2016), it remains beyond question that the observed change in the gene pool must have involved the migration of people. Moreover, the apparent abruptness with which this change occurred suggests that it was a large-scale migration event, rather than a slow periodic gene flow across many centuries.

The Yamnaya people from the Pontic-Caspian steppe are the best-known proxy for this incoming gene flow. The exact source could have been another, yet unsampled, group of people, but, in that case, they must have been very closely related genetically to Yamnaya.

The formation of the Yamnaya and Corded Ware Cultures
[...] Secondly, we should observe that Corded Ware Cultures co-existed with late Neolithic cultures for shorter or longer periods across much of Central and Northern Europe. In Denmark, there were late Funnel Beaker communities in the Danish islands (Iversen 2015); in other parts of Northern Europe they were often in close proximity, such as the Globular Amphora Culture in Poland (Szmyt 1999).

What we observe, therefore, in the archaeological record is a gradual process of acculturation and integration, which meant that after 2400 BC, the former strict cultural boundaries were gradually dissolved and a new, shared material culture appeared, represented first and foremost in Denmark by flint daggers, and in Central Europe by early Únetice metal daggers. Bell Beaker groups had by now also emerged on the scene, introducing metallurgy, and they further complicated the mix of cultures and people.

In burial rituals, however, old megalithic traditions still had an impact, as seen in a revival of stone cist burial in some regions. It was only on the advent of the Middle Bronze Age that cultural homogenisation prevailed. Thus, it took nearly 1000 years before all regions in Northern and Central Europe had adopted a shared social and cultural outlook that in all probability also included shared languages.[...]

Language dispersal and the formation of Proto-Germanic in northern Europe[...]

In their study on the formation of Proto-Germanic in Northern Europe, Kroonen and Iversen document a bundle of linguistic terms of non-Indo-European origin linked to agriculture that were adopted by Indo-European-speaking groups who were not fully fledged farmers. The most plausible, and perhaps the only possible, context for this to have happened would be the introduction of Proto-Germanic by the intruding Yamnaya groups.

Archaeologically, this adoption can be understood from their interaction over several hundred years with late Funnel Beaker groups still residing in eastern Jutland and on the Danish islands, where they maintained a largely agricultural economy.

From this we can conclude that terms linked to farming, and the cultivation of many important crops, were missing among the early Yamnaya/Corded Ware groups, who may well have acquired cereals (barley) mainly for the purpose of producing and consuming beer (Klassen 2005). In addition, we learn that the Neolithic language of the Funnel Beaker Culture was in all probability non-Indo-European. This process of language interaction is illustrated by the model in Figure 2. It illustrates that different Indo-European language branches were in contact with one and the same Neolithic tongue throughout Europe.

[...]From this we may conclude that Funnel Beaker societies spoke a non-IndoEuropean language, and thus another pillar in support of the Anatolian hypothesis of farming/language dispersal (Renfrew 1987) has fallen. When the whole complex of wagon terminology is taken into account, i.e. ‘wheel’, ‘axle’, ‘nave’, ‘thill’, ‘yoke’, ‘hame’ (Anthony & Ringe 2015: tab. 1, fig. 1), the idea that all of those terms arose independently in the daughter languages seems extremely unlikely.

When we add the evidence from ancient DNA, and the additional evidence from recent linguistic work discussed above, the Anatolian hypothesis must be considered largely falsified. Those Indo-European languages that later came to dominate in western Eurasia were those originating in the migrations from the Russian steppe during the third millennium BC.

Conclusion - We have been able to reconstruct the social processes of cultural integration and hybridisation that followed from (probable) Neolithic women marrying into Yamnaya settlements dominated by males of first-generation migrants. This practice continued over several generations, and the women soon started to produce new pottery versions of existing containers made of organic materials, with some further innovations. The original herding economy of the Yamnaya migrants gradually gave way to new agrarian practices of crop cultivation, which led to the adaptation of new words.

The result of this hybridisation process was the formation of a new material culture, the Corded Ware Culture, and of a new dialect, Proto-Germanic (or perhaps more correctly, Pre-Proto-Germanic). The latter was likewise an adaptation to new conditions, with the borrowing of novel terms from neighbouring Neolithic communities and from women who had married in to the migrant communities. Archaeology here provides a socio-linguistic setting for a process of language change over several hundred years between 2800 and 2400 BC.

This integrated model of cultural, linguistic and genetic change explains the formation of Corded Ware Cultures as a result of local adaptations and of interaction between migrant Yamnaya populations and indigenous Neolithic cultures. The social institution of exogamy provided an integrating mechanism, despite sometimes hostile relations between intruding Corded Ware groups and residing Neolithic groups; the burials at Eulau are the most prominent example of this.

Burial rituals also reveal a major difference in property relations and thus social organisation between existing Neolithic groups and intruding Yamnaya/Corded Ware groups. Both Yamnaya and Corded Ware groups shared individual burials under small family mounds, reflecting the transmission among individual families of animals and other property between generations.

In contrast to this, the collective, megalithic or similar type burials of Neolithic groups reflected collective, clan-like shared ownership of property, animals and land.

This collision of ideologies was played out gradually, with the Corded Ware political economy and interlinked cosmology as the winner once we enter the Bronze Age. Some influences from the Neolithic past, however, remained in both language and social organisation. This new historical interpretation rests on relatively solid ground, and represents a return to a more dramatic past than the prevailing model of cultural and technological transmissions. Some may not like it for its resemblance to an older paradigm of migrations as a primary cause of cultural change, as represented by Gustav Kossinna and Gordon Childe (Kristiansen 1998: 7–24), but we are now in a position to unravel the complexities behind the historical processes in much detail, and thus avoid the simplistic models of the past. Through this we realise that peaceful interaction and intermarriage between culturally and genetically different groups formed the day-to-day foundations of social life, interspersed with episodes of conflict.

In the long term, however, the Corded Ware social formation had the potential to dominate, not least when supported by the migrations of related Bell Beaker groups. Together, their social and demographic force would finally create the foundations for the rise of the Bronze Age. We are only beginning to understand these processes, however, and much new evidence can be expected that will add detail and refine our models, while retaining the big picture.

That Germanic has a substrate from hunter gatherers is nothing new: also, phenotypically a strong influence from local hunter gatherers was predicted because of "UP survivors" on the North German plain, leaning back to the Ertebolle and even Magdalenian populations, and comparable also to Mesolithic Ukrainians (ie. Vovnigy).

Germanic among IE branches is the odd man out, without including Germanic the tree is resolved fairly easily. Naturally this is because it is a contact language arising from a subarctic substrate and more than one branch of IE. Within IE languages, Germanic has similarities to the Celtic-Italic branch, Balto-Slavic and something like Albanian.

Indeed, the Germanic Substrate Hypothesis has found by the German linguist, Sigmund Feist. He had written that the Proto-German is a creol language what spoke the local Finno-Ugric inhabitants of Germany. He told that the few, but mighty Indo-European conquerors had forced own language to the local Finno-Ugrians, hence the nowadays Germanic languages full of unknown (probably Finno-Ugrain) worts.

Just a few example, the Indo-European word for water is the latin Aqua, but this basic word is in the Germanic languages is different, f.e. Water, Wasser and the Finno-Ugric words just te same, f.e.Finnish Vesi, Hungarian Víz. The Indo-European rooted words for house are the Latin Domus, Russian Dom, the Finno-Ugric rooted words in the Germanic languages are the House, Haus, the house in Finno-Ugric languages are the Finnish Kota, the Hungarian Ház. In the German language exist two word for the see, the Indo-European Meer and the Finno-Ugric See. Interestingly the most of word of the sailing are not from the Indo-European, f.e. See, Keel, Sail, etc.

So, Sigmund Feist's invention was very fantastic, however the idiot nazi authorities wanted not to hear that the German language is a kreol language of non-Germanic Finno-Ugrians and non-Germanic Indo-Europeans, hence they pursuited Sigmund Feist.

After the war this hypothesis rested in the drawer. Some dacades before present Colin Renfrew has maden the Anatolian Hypothesis what means the early Proto-Europeans have comen from the Middle-East and they carried the Neolithic cultur (agricultur, animal husbandry and own PIE language) to Europe. It was before the oldest human scripts, before the Sumerians or the Egyptians, probably 7–5 thousand before Christ.

Coon had written about the same time of the spread of the Mediterranid type from the Middle-East to Europe, hence probably Renfrew's PIEs were the carrier the Mediterranid genes what had spread across Europe from Hispania to the Ural, from Greece to Norway. The main centre of this Proto-Indo-Europeans was the Carpathian Basis where the basic and largest population nowadays Mediterranids too. This was the place were the Kentum (Western: Germanic, Italic, Keltic, Greek, Tocharic) and the Satem (Eastern: Baltic, Slavic, Caucasic, Indo-Iranian, Indic) dialects had diversed from the Proto Indo-European and they had found new homelands, where these languages had transformed to the Proto-Germanic, Proto-Greek, etc. languages.

In many places of Europe what conquer the Indo-Europeans they had melted to the local population, only their genes survived without the language. These places were like as the British-Islands where were Mediterranids before the Kelts, Romans or Germanics. They languages had disappeard among the Paleolithic populations of the British-Islands (Brünns, Borrebys). Another example is Norway, Tröndelag, where the Corded IEs had melted into the Finno-Ugrians and they waited till the Ancient Germanics whos have conquered Norway with own creol Proto-Germanics. The nowadays Trönder type is the mix of the early unkown Indo-Europeans from the Neolithic and the Germanic newcomers.

So, take a look to the Indo-European languages. I learnt in the University two ancient IE languages, the Latin and the more archaic Ancient Greek. I just see that how old an IE language, it have more and more some specific tendency. In the modern IE languages the sex of the nouns are disappearing. The sex of the nouns in the more archaic IE languages like as the Latin or the Ancient Greek are more stabil. In the modern IE languages the sign of the sex of the noun is the article, the have not suffix like as the latin masculine Domus (house) or the femine Ancilla (female servant). The modern German uses just articles (excluding the -s genitivus by masculin and neutral nouns). The sex of the nouns is a very ancient IE feature. Another typical IE feature is the flectation of the root of the world, f.e. swim, swam, swum. Another e. is the German word Burg (originally mountain fortress > castle, city) and Berg (mountain). A noun with different rootwovel means differents thing. Another example the sing. Goose > pl. Geese. Another specific feature the dual of the old IE languages. In the English and the German are only the words for dual, f.e. Both, Beide. In the old IE languages were a full line of dual nouns and dual verbs as two house or both we hunt, both you hunt, both they hunt

So the PIE had comen from the Middle-East, the Mediterranids had comen from in the same time from the Middle-East and the Neolithic culture had comen from the same from the Middle-East. Where is the population which had lived in the same time in the Middle-East, which had spoken a language with sex of nouns, flectation of the rootwovel of the word, using of dual nouns and verbs, which had known the Neolithic culture?

The oldest Sumerian scripts have told us that the neighbour of the Sumerians were the Akkads whos spoke the most archaic Semitic language what we know. They knewn the Neolithic culture too. They were Mediterranids too. Their language contains a very interesting network of using sex among the nouns and among the werbs too. F.e. nowadays Arab language can say with one word that "two female swam". Their language has the flectation, the change of the wovels of the root of the word too, f.e. Kitab (book), Katib (writer).

So it seems the Ancient Indo-Europeans were a branch of the Semitic tribes whos carry on an old Semitic language, the Neolithic cultur and the Mediterranid genepool too to the very rare inhabitated Finno-Ugric Middle-Europe where this language has divided to the old IE dialects what has spreaded across Europe with the Mediterranid Genepool and in several places of Europe the mixing of the languages of the conquerors and the natives had born the Proto-Germanic, Proto-Keltic, Proto-Greek, etc. languages. The Mediterranid genes have carried by the Indo-Europeans to every corner of the Continent. In some places, f.e. Norway they had forgotten own languages, just the newer conquer of the Ancient Germanics have brought their creol IE language to that location. In the way the IE mixed more and more among the local Cromagnonid rooted pre-Neolithic inhabitants, they have becomen lesser and lesser Mediterranid and more Cromagnonid, side by side they language more and more pigdinised by the local natives. Hence the southern part of the continent speak more archaic IE languages and the modern inhabitants mostly Mediterranid, but the northern inhabitants are more Cromagnonid and they speak a very pigdinised creol languages, f.e. the German or the Irish.

"Remember that, even when those who move you be kings or men of power, your soul is in your keeping alone. When you stand before God, you cannot say, "But I was told by others to do thus,"or that virtue "was not convenient at the time." This will not suffice."
/King Baldwin IV in the Kingdom of Heaven/

The common ancestor of the Hamitic and Semitic language has camen from the North-African plain what covered grassland, rivers and likes 7000 BC. That was the ultimate ancient homeland of the slender, high faced, high and long skulled, narrow and long nosed Mediterranid type what has spread till Kenya, Hispania, Norway and Malaysia too.

"Remember that, even when those who move you be kings or men of power, your soul is in your keeping alone. When you stand before God, you cannot say, "But I was told by others to do thus,"or that virtue "was not convenient at the time." This will not suffice."
/King Baldwin IV in the Kingdom of Heaven/

Well you are talking about the Atlanto-Med or Eurafrican or Protomed arriving in N Africa with the Capsians. Probably the upper Tuareg castes are the best examples: but you see it also in N Spain today, at Sumerian Kish etc. Wouldn't be surprised if the western branch of these spoke something like Basque. There is Basque vocabulary in (unclassifiable) Guanche and what seem to be Basque-like words in (IE: Italic) Sardinia and elsewhere. Vasconic as Mediterranean Neolithic?